00:00
What I would like to do now is go through and
describe each of the amino acids and point
out some salient features of them as appropriate.
The aromatic group of amino acids includes
tyrosine, tryptophan and phenylalanine. Now,
I've marked on the tyrosine, the locations
of the alpha carboxyl, the alpha amine and
the alpha carbon, and remind you again that
the hydrogen is projecting above but not shown
in this image. Tyrosine is noted has a hydroxyl
group attached to the end of benzene ring.
Tryptophan is notable for being an amino acid
that has the largest R group, contains a benzene
ring attached to another five-member ring
as you can see here. Now this very large bulky
group that's on tryptophan, tends to be a
limitation in terms of space within a protein.
The bulky R group can cause the protein to
have to twist and turn, and accommodate that
larger structure as a result. Phenylalanine
has a simple benzene ring.
01:03
Now what I've also done on this slide is I've
marked at physiological pH, the charges that
appear on each molecule. You'll see that in
each case the alpha carboxyl has a negative
charge because it has lost a proton. In each
case, the alpha amine has a positive charge
because it is retaining a proton. The pKa
of the alpha carboxyl group is about 2,
physiological pH of course is about 7.4. The
pKa of the alpha amine group is about 9,
so for this reason the alpha amine retains
the proton and the alpha carboxyl has lost
its proton. Now one note about tyrosine and that
is that the hydroxyl at the end of tyrosine
can ionize at a high pH, this pH is above
that of the physiological range however.
01:52
The second group of amino acids that I want
to talk about are those that
contain aliphatic R groups. In this case I've
marked again in the green squares each of the
R groups as they are contained in each amino
acid. Focusing on glycine for example, we
see glycine has an unusual R group, and that
it only contains a hydrogen. Glycine therefore
has the smallest R group of any of the naturally
occurring amino acids in proteins, but because
it contains an R group hydrogen and it also
contains the hydrogen that's attached to the
alpha carbon, it means that there're only three
different things attached to the alpha carbon
of glycine. For this reason glycine is the
only amino acid of the 20 that's found in
proteins that does not have a stereochemistry.
02:44
The next amino acid that is of interest is
proline. You can see the proline has an R
group that goes off of the alpha carbon, but
it also comes back around and connects with
the alpha amine as you can see forming a five-member
ring. Now this connection at two points limits
the ability of the R group of proline to rotate.
If you look at all of the other R groups of
all of the other proteins, you'll see they
only have a single bond and can freely rotate.
03:14
Proline is constrained by the second bond
that it's making with the alpha amino group
and as a consequence, proline cannot rotate
its R group, meaning that proline is a much
more inflexible amino acid. Now this has some
implications for bending that actually happens
within proteins as we will describe later.
03:35
The next three amino acids isoleucine, valine
and leucine are similar in containing R groups
that have carbons and hydrogens and mainly
rearrangements of those as you can see.
03:49
The last amino acid as shown here is methionine,
and methionine is of interest because methionine
contains sulfur. It's one of only two amino
acids that contain sulfur and the sulfur is
attached to two different carbons as you can
see in the grouping here. That attachment
to two different carbons means that the sulfur
in methionine is very unreactive and doesn't
do much, this is in contrast to the sulfur
that we will see in cysteine.
04:16
Now, if we look at the charges at physiological
pH, we can see that none of these amino acids
have R groups that ionize and like we saw
before the alpha amine has a plus charge in
each case and the alpha carboxyl has a negative
charge. Each of these amino acids at physiological
pH would have a charge of zero.
04:39
The next two amino acids are those that are ionized,
and they contain in their R groups, carboxyl
groups. They include aspartic acid, shown
on the left and glutamic acid, shown on the
right. These two amino acids are virtually
identical to each other with the exception
that glutamic acid contains one extra carbon
compared to aspartic acid. At physiological
pH we see here that the R group ionizes, and
this is because that the R group for these
two amino acids has a pKa value of about 4,
meaning that at a physiological pH of 7,
the proton on the carboxyl group is lost,
leaving the molecule with a net negative charge
on the R group. The overall charge of each
of these amino acids at physiological
pH is -1.